varroa ploidy

load libraries

library("tidyverse")
library("plyr")
library("dplyr")
library("ggplot2")
library("RColorBrewer")
#library("scales")
#library("ggpubr")
#library("gridExtra")
#library("grid")
#library("GGally")
library("data.table")
library("stringr")
library("janitor")
library("knitr")
library("kableExtra")
library("plotly") # for the 3d plots

knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
                 #    fig.width = 20,
                  #    fig.asp = 0.6,
                   #   out.width = "100%")

data <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa_ploidy/data/ploidy.csv") %>%
  dplyr::mutate(Family = as.character(Family))

# order the levels 
data$body.part <- factor(data$body.part, level=c("Body", "Anterior", "Posterior", "Legs","Hemolymph","Ovary","Testes"))

data$Stage <- factor(data$Stage, level=c("Larvae", "Protonymph", "Deuteronymph", "adult"))

p_fem = data %>% dplyr::filter(Sex == "fem") %>%
  dplyr::filter(body.part == c("Body", "Legs","Ovary","Testes")) %>%
  ggplot(aes(y=ploidy, x=body.part, fill = Sex)) + 
 geom_boxplot() +  theme_classic() +  geom_jitter(width=0.1, size=2) +
  facet_wrap(~Stage, nrow = 1) +  ggtitle('Female mite ploidy') +
  ylim(0, 3)

p_male = data %>% dplyr::filter(Sex == "male") %>%
  dplyr::filter(body.part == c("Body", "Legs","Ovary","Testes")) %>%
  ggplot(aes(y=ploidy, x=body.part, fill = Sex)) + 
 geom_boxplot(fill = "#00AFBB") +  theme_classic() +  geom_jitter(width=0.1, size=2,color = "#00AFBB",fill = "#00AFBB") +
  facet_wrap(~Stage, nrow = 1) +  ggtitle('Male mite ploidy') +
  ylim(0, 3)

p_adult = data %>% dplyr::filter(Stage == "adult") %>%
  ggplot(aes(y=ploidy, x=body.part, fill = Sex, lable = Stage)) + 
 geom_boxplot(outlier.shape = NA, coef=0 ) +  theme_classic() +  geom_jitter(width=0.1, size=2) +
  facet_wrap(~Sex)   + ggtitle('Adult mite ploidy') 

p_family = data %>% dplyr::filter(body.part == c("Body", "Ovary","Testes")) %>%
    mutate_at("Family", ~replace_na(.,"0")) %>%
  ggplot(aes(y=ploidy, x=Family, fill = Sex, lable = Stage)) + 
 geom_boxplot(outlier.shape = NA, coef=0 ) +  theme_classic() +  geom_jitter(width=0.1, size=2) +
  facet_wrap(~body.part, ncol = 1 )   + ggtitle('Adult mite ploidy per family') 


ggplotly(p_fem)

ggplotly(p_male)

ggplotly(p_adult)

ggplotly(p_family)